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I think you might need to be a bit more specific I've seen PDF files used loads of ways. Some of the most handy use bookmarks on the left hand side to form a collapsable index - very useful for finding your way round large documents.

I've also seen PDFs used as forms, and even as interactive packages by linking several PDF files together. Tis dead clever, and of course all done in Acrobat.

PDF files need Acrobat Reader to view (as you probably know), the only way to really display them is to post links to them. The PDF file will be displayed in the browser or Acrobat Reader if the software is installed.

Internet Explorer will display them in the browser itself, so frames might be a way to go. You could have your site menu or some key links in the left or top frame, and load the document into the bottom? That's how we manage the documents are on our Intranet, it seems to work.

If you want to lay out the PDF file itself differently? Simple answer, can't be done. You'd need to find the original file in whatever package you created it in, change it, then print it to PDF again. The thing about PDF files is that they're a cross platform, (virtually) software independant snap shot of a document, not an actual document. You can copy and paste bits of text (I think), but the feature is nowhere near powerful enough for what you're after.

(I know you don't want to change the PDF, I just re-read your last post, I just didn't want to delete that paragraph in case someone else finds it useful )

This is much more a design question than a technology specific one as I'd first thought. My best advice, experiment, see what works, but if you can, keep them "anchored" to the page linking to the document in some way. It saves users from getting 'lost' in the PDF and losing the website. When you're dealing with non-web-savvy users (like our staff) that's pretty important.